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88 lines
4.4 KiB
XML
88 lines
4.4 KiB
XML
<tool id="gd_select_snps" name="Select" version="1.0.0">
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<description>a specified number of SNPs</description>
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<command interpreter="python">
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select_snps.py "--input=$input" "--output=$output" "--chrlens_loc=${GALAXY_DATA_INDEX_DIR}/gd.chrlens.loc" "--num_snps=$num_snps"
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#if $override_metadata.choice == "0":
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"--ref_chrom_col=${input.metadata.ref}" "--ref_pos_col=${input.metadata.rPos}" "--species=${input.metadata.species}"
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#else
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"--ref_chrom_col=$ref_col" "--ref_pos_col=$rpos_col" "--species=$species"
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#end if
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</command>
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<inputs>
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<param format="tabular" name="input" type="data" label="Selected SNPS dataset"/>
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<param name="num_snps" type="integer" value="10" optional="false" min="1" label="Number of SNPs"/>
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<conditional name="override_metadata">
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<param name="choice" type="select" format="integer" label="choose columns">
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<option value="0" selected="true">No, get columns from metadata</option>
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<option value="1" >Yes, choose columns</option>
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</param>
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<when value="0">
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<!-- no options -->
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</when>
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<when value="1">
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<param name="ref_col" type="data_column" data_ref="input" numerical="false" label="Column with reference chromosome"/>
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<param name="rpos_col" type="data_column" data_ref="input" numerical="true" label="Column with reference position"/>
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<param name="species" type="select" label="Choose species">
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<options from_file="gd.species.txt">
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<column name="name" index="1"/>
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<column name="value" index="0"/>
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</options>
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</param>
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</when>
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</conditional>
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</inputs>
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<outputs>
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<data format="wsf" name="output" metadata_source="input"/>
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</outputs>
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<tests>
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<test>
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<param name="input" value="gd.sample.wsf" ftype="wsf"/>
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<param name="num_snps" value="5"/>
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<param name="choice" value="0"/>
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<output name="output" file="gd.select_snps.wsf"/>
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</test>
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</tests>
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<help>
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**What it does**
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It attempts to select a specified number of SNPs from the dataset, making them
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approximately uniformly spaced relative to the reference genome. The number
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actually selected may be slightly more than the specified number.
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-----
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**Example**
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- input file::
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chr2_75111355_75112576 314 A C L F chr2 75111676 C F 15 4 53 2 9 48 Y 96 0.369 0.355 0.396 0
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chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2
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chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0
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chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1
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chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0
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chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0
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chr18_50154905_50155664 304 A G Y C chr18 50155208 A Y 4 2 17 5 1 22 Y 8 0.022 0.996 0.128 0
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chr18_57379354_57380496 315 C T V V chr18 57379669 G V 11 0 60 9 6 62 Y 726 0.118 0.048 0.014 1
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chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0
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chr19_39866997_39874915 3117 C T P P chr19 39870110 C P 3 7 65 14 2 32 Y 6 0.321 0.911 0.462 4
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etc.
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- output file::
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chr2_75111355_75112576 314 A C L F chr2 75111676 C F 15 4 53 2 9 48 Y 96 0.369 0.355 0.396 0
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chr8_93901796_93905612 2471 A C A A chr8 93904264 A A 8 0 51 10 2 14 Y 961 0.016 0.534 0.114 2
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chr10_7434473_7435447 524 T C S S chr10 7435005 T S 11 5 90 14 0 69 Y 626 0.066 0.406 0.727 0
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chr14_80021455_80022064 138 G A H H chr14 80021593 G H 14 0 69 9 6 124 Y 377 0.118 0.997 0.195 1
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chr15_64470252_64471048 89 G A Y Y chr15 64470341 G Y 5 6 109 14 0 69 Y 312 0.247 0.998 0.393 0
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chr18_48070585_48071386 514 C T E K chr18 48071100 T K 7 7 46 14 0 69 Y 2 0.200 0.032 0.163 0
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chr19_14240610_14242055 232 C T A V chr19 14240840 C A 18 8 56 15 5 42 Y 73 0.003 0.153 0.835 0
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etc.
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</help>
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</tool>
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